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SEC24B SEC24 homolog B, COPII coat complex component [ Homo sapiens (human) ]

Gene ID: 10427, updated on 7-Apr-2024

Summary

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Official Symbol
SEC24Bprovided by HGNC
Official Full Name
SEC24 homolog B, COPII coat complex componentprovided by HGNC
Primary source
HGNC:HGNC:10704
See related
Ensembl:ENSG00000138802 MIM:607184; AllianceGenome:HGNC:10704
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SEC24
Summary
The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein is thought to be a cargo-binding component of the COPII vesicle, and is thought to be involved in the transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus. Mutations in this gene have been associated with neural tube defects, and are thought to be a result of a disruption in interactions with the protein encoded by the VANGL planar cell polarity protein 2 (VANGL2) gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in thyroid (RPKM 10.5), liver (RPKM 10.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4q25
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (109433815..109540896)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (112735946..112843029)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (110354971..110462052)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:110223886-110224668 Neighboring gene COL25A1 divergent transcript Neighboring gene RBMX pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:110314172-110314672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:110314673-110315173 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:110340209-110340746 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:110354865-110355724 Neighboring gene Sharpr-MPRA regulatory region 6018 Neighboring gene SEC24B antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:110374133-110374713 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71781 Neighboring gene RNA, 7SL, cytoplasmic 55, pseudogene Neighboring gene microRNA 576 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21802 Neighboring gene CDC42 pseudogene 4 Neighboring gene SET pseudogene 20

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration. Ryan SK, et al. Nat Neurosci, 2023 Jan. PMID 36536241, Free PMC Article
  2. Mutations in the COPII vesicle component gene SEC24B are associated with human neural tube defects. Yang XY, et al. Hum Mutat, 2013 Aug. PMID 23592378
  3. The role of the C-terminal domain of PCSK9 and SEC24 isoforms in PCSK9 secretion. Deng SJ, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2020 Jun. PMID 32058034
  4. The C-terminal domain of Kv1.3 regulates functional interactions with the KCNE4 subunit. Solé L, et al. J Cell Sci, 2016 Nov 15. PMID 27802162, Free PMC Article
  5. The sterol-sensing endoplasmic reticulum (ER) membrane protein TRC8 hampers ER to Golgi transport of sterol regulatory element-binding protein-2 (SREBP-2)/SREBP cleavage-activated protein and reduces SREBP-2 cleavage. Irisawa M, et al. J Biol Chem, 2009 Oct 16. PMID 19706601, Free PMC Article

See all (94) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration.
    Title: Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration.
  2. The role of the C-terminal domain of PCSK9 and SEC24 isoforms in PCSK9 secretion.
    Title: The role of the C-terminal domain of PCSK9 and SEC24 isoforms in PCSK9 secretion.
  3. results show that functional mutations in SEC24B might contribute to the etiology of a subset of human Neural Tube Defects (NTDs).
    Title: Mutations in the COPII vesicle component gene SEC24B are associated with human neural tube defects.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.
  5. Data show that coupling of the Sec23/24 and Sec13/31 layers of the COPII coat is required to drive export of collagen from the endoplasmic reticulum, and that efficient COPII assembly is essential for normal craniofacial development during embryogenesis.
    Title: Efficient coupling of Sec23-Sec24 to Sec13-Sec31 drives COPII-dependent collagen secretion and is essential for normal craniofacial development.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC48822

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in COPII-coated vesicle cargo loading IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in COPII-coated vesicle cargo loading IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in aorta morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in auditory receptor cell stereocilium organization IEA
Inferred from Electronic Annotation
more info
  
involved_in cochlear nucleus development IEA
Inferred from Electronic Annotation
more info
  
involved_in coronary artery morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in lung lobe morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in neural tube closure IEA
Inferred from Electronic Annotation
more info
  
involved_in outflow tract morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in pulmonary artery morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cargo loading into COPII-coated vesicle IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of establishment of planar polarity involved in neural tube closure IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of COPII vesicle coat IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of COPII vesicle coat IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ER to Golgi transport vesicle membrane TAS
Traceable Author Statement
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in endoplasmic reticulum exit site IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
protein transport protein Sec24B
Names
SEC24 related gene family, member B
secretory protein 24

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032166.1 RefSeqGene

    Range
    5001..112082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042734.4 → NP_001036199.1  protein transport protein Sec24B isoform b

    See identical proteins and their annotated locations for NP_001036199.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two in-frame exons in the 5' and central coding region, and uses an alternate in-frame splice site in the central coding region, compared to variant 3. The encoded isoform (b) is shorter, compared to isoform c.
    Source sequence(s)
    AC105314, BC040137, BC117135, H15283
    Consensus CDS
    CCDS43260.1
    UniProtKB/TrEMBL
    B4DTM6
    Related
    ENSP00000382051.2, ENST00000399100.6
    Conserved Domains (6) summary
    COG5028
    Location:428 → 1224
    COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
    cd01479
    Location:640 → 883
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:1105 → 1179
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:567 → 603
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:983 → 1078
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:884 → 968
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

  2. NM_001300813.3 → NP_001287742.1  protein transport protein Sec24B isoform c

    See identical proteins and their annotated locations for NP_001287742.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
    Source sequence(s)
    AC105314, BC040137, BC143268, H15283
    Consensus CDS
    CCDS75179.1
    UniProtKB/TrEMBL
    B4DTM6
    Related
    ENSP00000428564.1, ENST00000504968.6
    Conserved Domains (5) summary
    cd01479
    Location:705 → 948
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:1170 → 1244
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:632 → 668
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:1048 → 1143
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:949 → 1033
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

  3. NM_001318085.2 → NP_001305014.1  protein transport protein Sec24B isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region, compared to variant 3. The encoded isoform (d) is shorter, compared to isoform c.
    Source sequence(s)
    AC105314, BC040137, BC143269, H15283
    UniProtKB/TrEMBL
    B4DTM6
    Conserved Domains (5) summary
    cd01479
    Location:674 → 917
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:1139 → 1213
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:601 → 637
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:1017 → 1112
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:918 → 1002
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

  4. NM_001318086.2 → NP_001305015.1  protein transport protein Sec24B isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two in-frame exons in the 5' and central coding region, compared to variant 3. The encoded isoform (e) is shorter, compared to isoform c.
    Source sequence(s)
    AC105314, AK300278, BC040137, BC143269, H15283
    UniProtKB/TrEMBL
    B4DTM6
    Conserved Domains (5) summary
    cd01479
    Location:639 → 882
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:1104 → 1178
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:566 → 602
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:982 → 1077
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:883 → 967
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

  5. NM_006323.5 → NP_006314.2  protein transport protein Sec24B isoform a

    See identical proteins and their annotated locations for NP_006314.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the 5' coding region and uses an alternate in-frame splice site in the central coding region, compared to variant 3. The encoded isoform (a) is shorter, compared to isoform c.
    Source sequence(s)
    AC105314, BC040137, BC143268, H15283
    Consensus CDS
    CCDS47124.1
    UniProtKB/Swiss-Prot
    B7ZKM8, B7ZKN4, O95487, Q0VG08
    UniProtKB/TrEMBL
    B4DTM6
    Related
    ENSP00000265175.4, ENST00000265175.5
    Conserved Domains (6) summary
    COG5028
    Location:463 → 1259
    COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
    cd01479
    Location:675 → 918
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:1140 → 1214
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:602 → 638
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:1018 → 1113
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:919 → 1003
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    109433815..109540896
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007652.3 → XP_016863141.1  protein transport protein Sec24B isoform X10

    UniProtKB/TrEMBL
    B4DTM6

  2. XM_047449519.1 → XP_047305475.1  protein transport protein Sec24B isoform X11

  3. XM_011531536.4 → XP_011529838.1  protein transport protein Sec24B isoform X1

    UniProtKB/TrEMBL
    B4DTM6
    Conserved Domains (6) summary
    COG5028
    Location:439 → 1235
    COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
    cd01479
    Location:651 → 894
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:1116 → 1190
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:578 → 614
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:994 → 1089
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:895 → 979
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

  4. XM_047449514.1 → XP_047305470.1  protein transport protein Sec24B isoform X5

  5. XM_047449512.1 → XP_047305468.1  protein transport protein Sec24B isoform X3

  6. XM_047449513.1 → XP_047305469.1  protein transport protein Sec24B isoform X4

  7. XM_011531537.4 → XP_011529839.1  protein transport protein Sec24B isoform X2

    UniProtKB/TrEMBL
    B4DTM6
    Conserved Domains (6) summary
    COG5028
    Location:436 → 1232
    COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
    cd01479
    Location:648 → 891
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:1113 → 1187
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:575 → 611
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:991 → 1086
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:892 → 976
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

  8. XM_047449515.1 → XP_047305471.1  protein transport protein Sec24B isoform X6

  9. XM_047449516.1 → XP_047305472.1  protein transport protein Sec24B isoform X7

  10. XM_047449517.1 → XP_047305473.1  protein transport protein Sec24B isoform X8

  11. XM_047449518.1 → XP_047305474.1  protein transport protein Sec24B isoform X9

  12. XM_047449520.1 → XP_047305476.1  protein transport protein Sec24B isoform X12

  13. XM_047449521.1 → XP_047305477.1  protein transport protein Sec24B isoform X13

  14. XM_011531540.4 → XP_011529842.1  protein transport protein Sec24B isoform X14

    UniProtKB/TrEMBL
    B4E2E1
    Conserved Domains (5) summary
    cd01479
    Location:140 → 383
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:605 → 679
    Gelsolin; Gelsolin repeat
    pfam04810
    Location:67 → 103
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:483 → 578
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:384 → 468
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    112735946..112843029
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348758.1 → XP_054204733.1  protein transport protein Sec24B isoform X10

  2. XM_054348759.1 → XP_054204734.1  protein transport protein Sec24B isoform X11

  3. XM_054348749.1 → XP_054204724.1  protein transport protein Sec24B isoform X1

  4. XM_054348753.1 → XP_054204728.1  protein transport protein Sec24B isoform X5

  5. XM_054348751.1 → XP_054204726.1  protein transport protein Sec24B isoform X3

  6. XM_054348752.1 → XP_054204727.1  protein transport protein Sec24B isoform X4

  7. XM_054348750.1 → XP_054204725.1  protein transport protein Sec24B isoform X2

  8. XM_054348754.1 → XP_054204729.1  protein transport protein Sec24B isoform X6

  9. XM_054348755.1 → XP_054204730.1  protein transport protein Sec24B isoform X7

  10. XM_054348756.1 → XP_054204731.1  protein transport protein Sec24B isoform X8

  11. XM_054348757.1 → XP_054204732.1  protein transport protein Sec24B isoform X9

  12. XM_054348760.1 → XP_054204735.1  protein transport protein Sec24B isoform X12

  13. XM_054348761.1 → XP_054204736.1  protein transport protein Sec24B isoform X13

  14. XM_054348762.1 → XP_054204737.1  protein transport protein Sec24B isoform X14

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95487.2 GenPept UniProtKB/Swiss-Prot:O95487

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